Data from: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits has been well documented, additional sources of variation – such as the production of alternative RNA transcripts from a single gene, or isoforms – have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in the evolution of cryptic colour phenotypes in deer mice (genus Peromyscus). We first characterize the Agouti isoforms expressed in the Peromyscus skin and find two novel isoforms not previously identified in Mus. Next, we show that a locally adapted light-coloured population of P. maniculatus living on the Nebraska Sand Hills shows an upregulation of a single Agouti isoform, termed 1C, compared with their ancestral dark-coloured conspecifics. Using in vitro assays, we show that this preference for isoform 1C may be driven by isoform-specific differences in translation. In addition, using an admixed population of wild-caught mice, we find that variation in overall Agouti expression maps to a region near exon 1C, which also has patterns of nucleotide variation consistent with strong positive selection. Finally, we show that the independent evolution of cryptic light pigmentation in a different species, P. polionotus, has been driven by a preference for the same Agouti isoform. Together, these findings present an example of the role of alternative transcript processing in adaptation and demonstrate molecular convergence at the level of isoform regulation.进化生物学的核心目标之一，是解析介导表型适应的分子机制。尽管编码蛋白质的突变与顺式调控突变（cis-regulatory mutations）对适应性性状的贡献已得到广泛证实，但其他变异来源——例如从单个基因产生的可变RNA转录本（alternative RNA transcripts）或转录异构体（isoforms）——的研究仍相对不足。本研究以已知可表达多种可变转录本的色素基因Agouti为研究对象，探讨转录异构体使用在鹿鼠（Peromyscus属）隐蔽体色表型演化中的功能。我们首先对鹿鼠皮肤中表达的Agouti转录异构体进行了系统表征，发现了两种此前在小家鼠（Mus属）中未被鉴定的新型转录异构体。随后我们证实，栖息于内布拉斯加沙丘的适应性浅色鹿鼠（P. maniculatus）种群，相较于其祖先类群的深色同种个体，显著上调了单个被命名为1C的Agouti转录异构体的表达水平。通过体外功能实验，我们发现这种对1C型转录异构体的表达偏好，可能源于不同转录异构体在翻译过程中的特异性差异。此外，利用野生捕获的混血小鼠种群，我们发现Agouti基因总表达量的变异位点定位于外显子1C附近的基因组区域，该区域的核苷酸变异模式也符合强正向选择的特征。最后我们证实，另一物种海滩鹿鼠（P. polionotus）独立演化出的隐蔽浅色体色表型，同样由对同一Agouti转录异构体的表达偏好所驱动。综上，本研究为可变转录本加工在生物适应中的作用提供了一个典型实例，并证实了转录异构体调控层面的分子趋同演化现象。